rs17122830

Variant names:

• chr12-59679459-A-G
• rs17122830
• NM_001270623.2:c.-31+24209A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270623.2(SLC16A7):​c.-31+24209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,236 control chromosomes in the GnomAD database, including 429 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.071 (429 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 3 publications found

Genes affected

SLC16A7 (HGNC:10928): (solute carrier family 16 member 7) This gene is a member of the monocarboxylate transporter family. Members in this family transport metabolites, such as lactate, pyruvate, and ketone bodies. The protein encoded by this gene catalyzes the proton-linked transport of monocarboxylates and has the highest affinity for pyruvate. This protein has been reported to be more highly expressed in prostate and colorectal cancer specimens when compared to control specimens. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.-31+24209A>G		intron_variant	Intron 2 of 5	ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.-31+24209A>G		intron_variant	Intron 2 of 5	1	NM_001270623.2	ENSP00000448071.1

Frequencies

GnomAD3 genomes AF: 0.0712 AC: 10834 AN: 152118 Hom.: 429 Cov.: 32

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0272

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0856

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0712 AC: 10836 AN: 152236 Hom.: 429 Cov.: 32 AF XY: 0.0703 AC XY: 5233 AN XY: 74442

African (AFR) AF: 0.0991 AC: 4115 AN: 41520

American (AMR) AF: 0.0550 AC: 842 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3468

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5180

South Asian (SAS) AF: 0.103 AC: 497 AN: 4818

European-Finnish (FIN) AF: 0.0272 AC: 289 AN: 10622

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0627 AC: 4263 AN: 68008

Other (OTH) AF: 0.0833 AC: 176 AN: 2112

Alfa AF: 0.0693 Hom.: 500

Bravo AF: 0.0723

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.66
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17122830; hg19: chr12-60073240;